The MDMM 2008 meeting was devoted to discussions and presentations of current computational methods and their applications in molecular modeling, design of molecular materials, and related fields. This conference continues a tradition of alternating Polish-Czech (+American) meetings that have taken place in the Czech Republic and Poland since 2003. The MDMM2008 meeting in Piechowice, Poland included the following sessions: advances in computational methods, designed biomaterials, drug design, interactions in molecular materials, modeling biomaterials, zeolites, chemical reactions, nucleic acids, protein dynamics, and structure prediction (for more details see http://mml.ch.pwr.wroc.pl/workshop/2008/).